* Licensed to the Apache Software Foundation (ASF) under one

* or more contributor license agreements.  See the NOTICE file

* distributed with this work for additional information

* regarding copyright ownership.  The ASF licenses this file

* to you under the Apache License, Version 2.0 (the

* "License"); you may not use this file except in compliance

* with the License.  You may obtain a copy of the License at

*

*   http://www.apache.org/licenses/LICENSE-2.0

*

* Unless required by applicable law or agreed to in writing,

* software distributed under the License is distributed on an

* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY

* KIND, either express or implied.  See the License for the

* specific language governing permissions and limitations

* under the License.

*/

    // LOG4J logger based on class name

    private Logger logger = Logger.getLogger(getClass().getName());

    private UimaContext uimaContext;

    @Override

    public void initialize(UimaContext aContext) throws ResourceInitializationException {

      super.initialize(aContext);

      uimaContext = aContext;

      logger.info("Initializing " +  TemplateFillerAnnotator.class.getName());

 

    }

    /**

     * Copy values from <tt>original</tt> to <tt>mention</tt> and add <tt>mention</tt> to the indexes.

     * If <tt>original</tt> is a MedicationEventMention (which used to be created by ctakes-drug-ner),

     * create a MedicationMention from the MedicationEventMention, setting the MedicationMention specific

     * attributes like dosage from the MedicationEventMention attributes.

     * @param mention The annotation to copy values to

     * @param original The annotation to copy values from

     * @throws CASException

     */

    private void setAttributesFromOriginal(IdentifiedAnnotation mention, IdentifiedAnnotation original) throws CASException {

      mention.setBegin(original.getBegin());

      mention.setEnd(original.getEnd());

      mention.setConditional(original.getConditional());

      mention.setConfidence(original.getConfidence());

      mention.setDiscoveryTechnique(original.getDiscoveryTechnique());

      mention.setGeneric(original.getGeneric());

      mention.setOntologyConceptArr(original.getOntologyConceptArr());

      mention.setPolarity(original.getPolarity());

      mention.setSegmentID(original.getSegmentID());

      mention.setSentenceID(original.getSentenceID());

      mention.setSubject(original.getSubject());

      mention.setTypeID(original.getTypeID());

      mention.setUncertainty(original.getUncertainty());

      mention.setHistoryOf(original.getHistoryOf());

     

      if (original instanceof MedicationEventMention) {

        MedicationEventMention medEventMention = (MedicationEventMention) original;

        MedicationMention medMention = (MedicationMention) mention;

        JCas jcas = medMention.getCAS().getJCas();

        if (medEventMention.getStartDate()!=null) {

          Date date = medEventMention.getStartDate();

          TimeMention timeMention = new TimeMention(jcas);

          timeMention.setDate(date);

          medMention.setStartDate(timeMention);

        }

        if (medEventMention.getEndDate()!=null) {

          Date date = medEventMention.getEndDate();

          TimeMention timeMention = new TimeMention(jcas);

          timeMention.setDate(date);

          medMention.setEndDate(timeMention);

        }

        if (medEventMention.getMedicationDosage()!=null) {

          MedicationDosage dosage = medEventMention.getMedicationDosage();

          MedicationDosageModifier medDosageModifier = new MedicationDosageModifier(jcas);

          medDosageModifier.setNormalizedForm(dosage);

          medDosageModifier.setCategory(dosage.getValue());

          medMention.setMedicationDosage(medDosageModifier);

         

        }

        if (medEventMention.getMedicationDuration()!=null) {

          MedicationDuration duration = medEventMention.getMedicationDuration();

          MedicationDurationModifier medDurationModifier = new MedicationDurationModifier(jcas);

          medDurationModifier.setNormalizedForm(duration);

          medDurationModifier.setCategory(duration.getValue());

          medMention.setMedicationDuration(medDurationModifier);

        }

        if (medEventMention.getMedicationForm()!=null) {

          MedicationForm form = medEventMention.getMedicationForm();

          MedicationFormModifier medFormModifier = new MedicationFormModifier(jcas);

          medFormModifier.setNormalizedForm(form);

          medFormModifier.setCategory(form.getValue());

          medMention.setMedicationForm(medFormModifier);

        }

        if (medEventMention.getMedicationFrequency()!=null) {

          MedicationFrequency frequency = medEventMention.getMedicationFrequency();

          MedicationFrequencyModifier medFrequencyModifier = new MedicationFrequencyModifier(jcas);

          medFrequencyModifier.setNormalizedForm(frequency);

          medFrequencyModifier.setCategory(frequency.getNumber() + frequency.getUnit());

          medMention.setMedicationFrequency(medFrequencyModifier);

        }

        if (medEventMention.getMedicationRoute()!=null) {

          MedicationRoute route = medEventMention.getMedicationRoute();

          MedicationRouteModifier medRouteModifier = new MedicationRouteModifier(jcas);

          medRouteModifier.setNormalizedForm(route);

          medRouteModifier.setCategory(route.getValue());

          medMention.setMedicationRoute(medRouteModifier);

        }

        if (medEventMention.getMedicationStatusChange()!=null) {

          MedicationStatusChange statusChange = medEventMention.getMedicationStatusChange();

          MedicationStatusChangeModifier medStatusChangeModifier = new MedicationStatusChangeModifier(jcas);

          medStatusChangeModifier.setNormalizedForm(statusChange);

          medStatusChangeModifier.setCategory(statusChange.getValue());

          medMention.setMedicationStatusChange(medStatusChangeModifier);

        }

        if (medEventMention.getMedicationStrength()!=null) {

          MedicationStrength strength = medEventMention.getMedicationStrength();

          MedicationStrengthModifier medStrengthModifier = new MedicationStrengthModifier(jcas);

          medStrengthModifier.setNormalizedForm(strength);

          medStrengthModifier.setCategory(strength.getNumber() + strength.getUnit());

          medMention.setMedicationStrength(medStrengthModifier);

        }

       

        // TODO handle MedicationAllergyModifier here when / if the value is set/disovered some day

       

      }

      mention.addToIndexes();

     

    }

    @Override

    public void process(JCas jcas) throws AnalysisEngineProcessException {

 

  logger.debug("process(JCas) in " + TemplateFillerAnnotator.class.getName());

 

  // Get all IdentifiedAnnotations

  FSIterator<Annotation> identifiedAnnotationsIter = getAllAnnotations(jcas, IdentifiedAnnotation.type);

  Map<IdentifiedAnnotation, IdentifiedAnnotation> mapToMentions = new HashMap<IdentifiedAnnotation, IdentifiedAnnotation>();

  // For each IdentifiedAnnotations, if it is of one of the right types, copy to the appropriate new subtype

  List<Annotation> annotationsToRemoveFromCas = new ArrayList<Annotation>();

  try {

    while (identifiedAnnotationsIter.hasNext()) {

      IdentifiedAnnotation original = (IdentifiedAnnotation)identifiedAnnotationsIter.next();

      IdentifiedAnnotation mention = null;

      // for 3.0 and earlier, needed to map mentions to the more specific types. in post-3.0, already creating proper type

        // for things other than medications. Drug NER was creating MedicationEventMentions still for a while (in trunk)

        int t = original.getTypeID();

        if (t==CONST.NE_TYPE_ID_ANATOMICAL_SITE || t==CONST.NE_TYPE_ID_DISORDER || t==CONST.NE_TYPE_ID_DISORDER

            || t==CONST.NE_TYPE_ID_FINDING || t==CONST.NE_TYPE_ID_PROCEDURE) {

          mapToMentions.put(original, original); // with 3.1 don't need to map to proper mention type, already creating as proper type

        } else if (t==CONST.NE_TYPE_ID_DRUG) {

          // Drug NER (ctakes-drug-ner) was creating MedicationEventMention,

          // if found, create MedicationMention with its attributes based on the MedicationEventMention attributes

          if (original instanceof MedicationEventMention) {

            mention = new MedicationMention(jcas);

            mapToMentions.put(original, mention);

            setAttributesFromOriginal(mention, original);

            annotationsToRemoveFromCas.add(original);

          }

        }  else {

          // Some other type of IdentifiedAnnotation such as TimeMention, Modifier, DateMention, RomanNumeralAnnotation, etc

          // For each those we do nothing in this annotator.

        }

    }

  } catch (CASException e) {

    throw new AnalysisEngineProcessException(e);

  }

 

  // Fill in template slots from relations.

 

  //FSIndex<FeatureStructure> relationArgs = jcas.getFSIndexRepository().getIndex("_org.apache.ctakes.typesystem.type.relation.RelationArgument_GeneratedIndex");

  //FSIndex<FeatureStructure> binaryTextRelations = jcas.getFSIndexRepository().getIndex("_org.apache.ctakes.typesystem.type.relation.BinaryTextRelation_GeneratedIndex");

  FSIndex<FeatureStructure> locationOfTextRelations = jcas.getFSIndexRepository().getIndex("_org.apache.ctakes.typesystem.type.relation.LocationOfTextRelation_GeneratedIndex");

  FSIndex<FeatureStructure> degreeOfTextRelations = jcas.getFSIndexRepository().getIndex("_org.apache.ctakes.typesystem.type.relation.DegreeOfTextRelation_GeneratedIndex");

  int i = 0;

 

  if (locationOfTextRelations != null) {

   

      for (FeatureStructure binaryTextRelationFS: locationOfTextRelations) {

       

        i++;

        //logger.info("binaryTextRelationFS = " + binaryTextRelationFS);

        BinaryTextRelation binaryTextRelation = (BinaryTextRelation) binaryTextRelationFS;

        LocationOfTextRelation locationOfTextRelation = null;

        if (binaryTextRelation instanceof LocationOfTextRelation) {

          locationOfTextRelation = (LocationOfTextRelation) binaryTextRelationFS;

        }

       

        RelationArgument arg1 = binaryTextRelation.getArg1(); // an EntityMention  OR  location

        RelationArgument arg2 = binaryTextRelation.getArg2(); // a Modifier  OR   what is located at location

        String relation = binaryTextRelation.getCategory(); // "degree_of", "location_of"

        if (relation.equals("degree_of")) {

         

          // do nothing here, this loop is for dealing with location_of

          // degree_of has its own loop.

         

        } else if (relation.equals("location_of")) {

          IdentifiedAnnotation arg1Arg = (IdentifiedAnnotation) arg1.getArgument();

          IdentifiedAnnotation ia = mapToMentions.get(arg1Arg);

          if (ia instanceof EntityMention) {

           

            // Note you apparently can have an AnatomicalSiteMention be the location_of an AnatomicalSiteMention

            // from running rec041, end up with things like "Left lower extremity"  location_of "common femoral vein"

            // and "left renal vein" in relation location_of to anatomical site mention "renal vein"

            // and "vein" in relation location_of to anatomical site mention "renal vein"

            EntityMention entityMention = (EntityMention) ia;

            IdentifiedAnnotation location = (IdentifiedAnnotation) arg2.getArgument();

            IdentifiedAnnotation loc = (IdentifiedAnnotation)mapToMentions.get(location);

            if (loc instanceof AnatomicalSiteMention) {

              AnatomicalSiteMention asm = (AnatomicalSiteMention) loc;

              //asm.setBodyLocation(binaryTextRelation); // uncomment iff AnatomicalSiteMention ends up with a bodyLocation attribute

            } else {

              logger.error("Need to implement cases for handling EntityMention " + entityMention + " within relation: " + relation);

              logger.error("   loc " + loc + " in relation " + relation + " with/to " + entityMention);

              logger.error("   Using covered text: loc " + loc.getCoveredText() + " in relation " + relation + " with/to " + entityMention.getCoveredText());

            }

          } else {

           

            EventMention eventMention = (EventMention) ia;

            if (eventMention instanceof DiseaseDisorderMention) { //(eventMention.getTypeID()==CONST.NE_TYPE_ID_DISORDER) {

              DiseaseDisorderMention ddm = (DiseaseDisorderMention) eventMention;

              ddm.setBodyLocation(locationOfTextRelation);

            } else if (eventMention instanceof ProcedureMention) { //(eventMention.getTypeID()==CONST.NE_TYPE_ID_PROCEDURE) {

              ProcedureMention pm = (ProcedureMention) eventMention;

              pm.setBodyLocation(locationOfTextRelation);

            } else if (eventMention instanceof SignSymptomMention) { //(eventMention.getTypeID()==CONST.NE_TYPE_ID_FINDING) {

              SignSymptomMention ssm = (SignSymptomMention) eventMention;

              ssm.setBodyLocation(locationOfTextRelation);

            } else {

              logger.error("Need to implement more cases for handling EventMention " + eventMention + " within relation: " + relation);

            }

           

          }

        } else {

          logger.error("Need to implement more cases for relation: " + relation);

        }

      }

  }

 

  if (degreeOfTextRelations != null) {

   

      for (FeatureStructure binaryTextRelationFS: degreeOfTextRelations) {

       

        i++;

        //logger.info("binaryTextRelationFS = " + binaryTextRelationFS);

        BinaryTextRelation binaryTextRelation = (BinaryTextRelation) binaryTextRelationFS;

        DegreeOfTextRelation degreeOfTextRelation = null;

        if (binaryTextRelation instanceof DegreeOfTextRelation) {

          degreeOfTextRelation = (DegreeOfTextRelation) binaryTextRelationFS;

        }

       

        RelationArgument arg1 = binaryTextRelation.getArg1(); // an EntityMention  OR  location

        RelationArgument arg2 = binaryTextRelation.getArg2(); // a Modifier  OR   what is located at location

        String relation = binaryTextRelation.getCategory(); // "degree_of", "location_of"

        if (relation.equals("degree_of")) {

         

          Modifier severity = (Modifier) arg2.getArgument();

          // degree_of is aka severity, which applies to SignSymptomMention/SignSymptom and DiseaseDisorder

          // find Mention associated with arg1

          IdentifiedAnnotation arg1Arg = (IdentifiedAnnotation) arg1.getArgument();

          // set severity within the Mention to be arg2 (the Modifier)

          // Note at this point mapToMentions.get(entityMention) might be an entityMention instead of an EventMention

          // for example rec041 in the seed set resulted in

          //  ClassCastException: org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention

          //  cannot be cast to org.apache.ctakes.typesystem.type.textsem.EventMention

          IdentifiedAnnotation ia = mapToMentions.get(arg1Arg);

          if (ia instanceof EntityMention) {

            EntityMention entityMention = (EntityMention) ia;

            logger.error("Need to implement cases for handling EntityMention " + entityMention + " within relation: " + relation);

            logger.error("   severity " + severity + " in relation " + relation + " with/to " + entityMention);

            logger.error("   Using covered text: severity " + severity.getCoveredText() + " in relation " + relation + " with/to " + entityMention.getCoveredText());

          } else {

            EventMention eventMention = (EventMention) ia;

            if (eventMention instanceof DiseaseDisorderMention) {

              DiseaseDisorderMention ddm = (DiseaseDisorderMention) eventMention;

              ddm.setSeverity(degreeOfTextRelation);

            } else if (eventMention instanceof SignSymptomMention) {

              SignSymptomMention ssm = (SignSymptomMention) eventMention;

              ssm.setSeverity(degreeOfTextRelation);

            } else {

              logger.error("Need to implement more cases for handling EventMention " + eventMention + " within relation: " + relation);

            }

          }

         

        } else if (relation.equals("location_of")) {

          // do nothing here, this loop is for dealing with degree_of

          // location_of has its own loop.

         

        } else {

          logger.error("Need to implement more cases for relation: " + relation);

        }

      }

  }  

 

    }

    private FSIterator<Annotation> getAllAnnotations(JCas jcas, int type) {

  JFSIndexRepository indexes = jcas.getJFSIndexRepository();

  FSIterator<Annotation> annotationsIter = indexes.getAnnotationIndex(type).iterator();

        //  while (segmentItr.hasNext()) {

        //  }

  return annotationsIter;

    }

}